I have a program where I do a

manual plane

Level,

manual ID

Origin

sync CAD

then move the probe to the location of Datum E and instruct the operator to rotate the part so datum E lines up with the probe.

DCC plane, circle, Datum E

Level, Align, Origin

run time align part

sync CAD

Over time the location where the probe moves to keeps changing and the nominals for E in the program change with it.  When I report the location of E and the other holes the nominals reported are correct.  The problem is there is an angled hole that should be in the YZ plane but when E is at 4 O'Clock instead of 3Oclock it isn't and the probe angle no longer matches.

Why does this happen and what can I do to prevent it?